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Aktürk Dizman Y. Analysis of codon usage bias of exonuclease genes in invertebrate iridescent viruses. Virology 2024; 593:110030. [PMID: 38402641 DOI: 10.1016/j.virol.2024.110030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/04/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
Invertebrate iridescent viruses (IIVs) are double-stranded DNA viruses that belong to the Iridoviridae family. IIVs result diseases that vary in severity from subclinical to lethal in invertebrate hosts. Codon usage bias (CUB) analysis is a versatile method for comprehending the genetic and evolutionary aspects of species. In this study, we analyzed the CUB in 10 invertebrate iridescent viruses exonuclease genes by calculating and comparing the nucleotide contents, effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and others. The results revealed that IIVs exonuclease genes are rich in A/T. The ENC analysis displayed a low codon usage bias in IIVs exonuclease genes. ENC-plot, neutrality plot, and parity rule 2 plot demonstrated that besides mutational pressure, other factors like natural selection, dinucleotide content, and aromaticity also contributed to CUB. The findings could enhance our understanding of the evolution of IIVs exonuclease genes.
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Affiliation(s)
- Yeşim Aktürk Dizman
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, 53100, Rize, Türkiye.
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2
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Yiping L, Chien T, Chiehhao W, Iwen C, Mingchu C. Emergence of Decapod iridescent virus 1 in cultured shrimp from Taiwan in 2020. Vet Med Sci 2023; 9:2336-2341. [PMID: 37471582 PMCID: PMC10508494 DOI: 10.1002/vms3.1216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 10/26/2022] [Accepted: 07/06/2023] [Indexed: 07/22/2023] Open
Abstract
OBJECTIVES This study was to identify and characterize Decapod iridescent virus 1 (DIV1) in the outbreaks reported in two whiteleg shrimp farms and one black tiger shrimp farm located in northern Taiwan in 2020. METHODS The histopathology, electron microscopy and polymerase chain reaction (PCR) specific for the DIV1 were used to identify the virus, and the phylogenetic analysis was performed by comparing the major capsid protein gene fragment of DIV1s from Taiwan with reference sequences of the family Iridoviridae. RESULTS DIV1 was identified by diagnostic PCR and caused mild mortality (20%) in cultured Penaeus monodon and high mortality (100%) in cultured whiteleg shrimp. Cultured P. monodon was first found to be infected with DIV1 through natural route of infection. Histopathological examination showed dark-eosinophilic cytoplasmic inclusions in the degenerative cells of targeted hematopoietic tissues. For electron microscopy, a non-enveloped virus particle was observed from homogenates of mixed target organs through negative staining with a diameter of 112±2 nm. Nucleotide sequences of DIV1 isolates from the Taiwanese outbreak are 100% identical to those from the PRC. CONCLUSIONS Based on the clinical evidence, mortality rates, histopathology, electron microscopy examinations and phylogenetic analysis, it is believed that DIV1 is the causative agent of the outbreak. This is the first report of DIV1 in cultured shrimp in Taiwan. The emergence of DIV1 signals a warning to shrimp aquaculture farmers worldwide.
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Affiliation(s)
- Lu Yiping
- Aquatic Medicine Laboratory, Biology DivisionAnimal Health Research InstituteCouncil of AgricultureNew Taipei CityTaiwanRepublic of China
- Department of Veterinary MedicineNational Pingtung University of Science and TechnologyPingtungTaiwanRepublic of China
| | - Tu Chien
- Aquatic Medicine Laboratory, Biology DivisionAnimal Health Research InstituteCouncil of AgricultureNew Taipei CityTaiwanRepublic of China
| | - Wu Chiehhao
- Aquatic Medicine Laboratory, Biology DivisionAnimal Health Research InstituteCouncil of AgricultureNew Taipei CityTaiwanRepublic of China
| | - Chen Iwen
- Aquatic Medicine Laboratory, Biology DivisionAnimal Health Research InstituteCouncil of AgricultureNew Taipei CityTaiwanRepublic of China
| | - Cheng Mingchu
- Department of Veterinary MedicineNational Pingtung University of Science and TechnologyPingtungTaiwanRepublic of China
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3
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Wallace MA, Coffman KA, Gilbert C, Ravindran S, Albery GF, Abbott J, Argyridou E, Bellosta P, Betancourt AJ, Colinet H, Eric K, Glaser-Schmitt A, Grath S, Jelic M, Kankare M, Kozeretska I, Loeschcke V, Montchamp-Moreau C, Ometto L, Onder BS, Orengo DJ, Parsch J, Pascual M, Patenkovic A, Puerma E, Ritchie MG, Rota-Stabelli O, Schou MF, Serga SV, Stamenkovic-Radak M, Tanaskovic M, Veselinovic MS, Vieira J, Vieira CP, Kapun M, Flatt T, González J, Staubach F, Obbard DJ. The discovery, distribution, and diversity of DNA viruses associated with Drosophila melanogaster in Europe. Virus Evol 2021; 7:veab031. [PMID: 34408913 PMCID: PMC8363768 DOI: 10.1093/ve/veab031] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Drosophila melanogaster is an important model for antiviral immunity in arthropods, but very few DNA viruses have been described from the family Drosophilidae. This deficiency limits our opportunity to use natural host-pathogen combinations in experimental studies, and may bias our understanding of the Drosophila virome. Here, we report fourteen DNA viruses detected in a metagenomic analysis of 6668 pool-sequenced Drosophila, sampled from forty-seven European locations between 2014 and 2016. These include three new nudiviruses, a new and divergent entomopoxvirus, a virus related to Leptopilina boulardi filamentous virus, and a virus related to Musca domestica salivary gland hypertrophy virus. We also find an endogenous genomic copy of galbut virus, a double-stranded RNA partitivirus, segregating at very low frequency. Remarkably, we find that Drosophila Vesanto virus, a small DNA virus previously described as a bidnavirus, may be composed of up to twelve segments and thus represent a new lineage of segmented DNA viruses. Two of the DNA viruses, Drosophila Kallithea nudivirus and Drosophila Vesanto virus are relatively common, found in 2 per cent or more of wild flies. The others are rare, with many likely to be represented by a single infected fly. We find that virus prevalence in Europe reflects the prevalence seen in publicly available datasets, with Drosophila Kallithea nudivirus and Drosophila Vesanto virus the only ones commonly detectable in public data from wild-caught flies and large population cages, and the other viruses being rare or absent. These analyses suggest that DNA viruses are at lower prevalence than RNA viruses in D.melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redressing an earlier bias toward RNA virus studies in Drosophila, and lay the foundation needed to harness the power of Drosophila as a model system for the study of DNA viruses.
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Affiliation(s)
- Megan A Wallace
- The European Drosophila Population Genomics Consortium (DrosEU)
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Kelsey A Coffman
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Clément Gilbert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Sanjana Ravindran
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Gregory F Albery
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Jessica Abbott
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Section for Evolutionary Ecology, Lund University, Sölvegatan 37, Lund 223 62, Sweden
| | - Eliza Argyridou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Paola Bellosta
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Cellular, Computational and Integrative Biology, CIBIO University of Trento, Via Sommarive 9, Trento 38123, Italy
- Department of Medicine & Endocrinology, NYU Langone Medical Center, 550 First Avenue, New York, NY 10016, USA
| | - Andrea J Betancourt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Hervé Colinet
- The European Drosophila Population Genomics Consortium (DrosEU)
- UMR CNRS 6553 ECOBIO, Université de Rennes1, Rennes, France
| | - Katarina Eric
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute for Biological Research “Sinisa Stankovic”, National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia
| | - Amanda Glaser-Schmitt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Sonja Grath
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Mihailo Jelic
- The European Drosophila Population Genomics Consortium (DrosEU)
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, Serbia
| | - Maaria Kankare
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Iryna Kozeretska
- The European Drosophila Population Genomics Consortium (DrosEU)
- National Antarctic Scientific Center of Ukraine, 16 Shevchenko Avenue, Kyiv, 01601, Ukraine
| | - Volker Loeschcke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Genetics, Ecology and Evolution, Aarhus University, Ny Munkegade 116, Aarhus C DK-8000, Denmark
| | - Catherine Montchamp-Moreau
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Lino Ometto
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy
| | - Banu Sebnem Onder
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Dorcas J Orengo
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - John Parsch
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Marta Pascual
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Aleksandra Patenkovic
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute for Biological Research “Sinisa Stankovic”, National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia
| | - Eva Puerma
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Michael G Ritchie
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, St Andrews University, St Andrews HY15 4SS, UK
| | - Omar Rota-Stabelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Research and Innovation Center, Fondazione E. Mach, San Michele all’Adige (TN) 38010, Italy
- Centre Agriculture Food Environment, University of Trento, San Michele all’Adige (TN) 38010, Italy
| | - Mads Fristrup Schou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Section for Evolutionary Ecology, Lund University, Sölvegatan 37, Lund 223 62, Sweden
- Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Svitlana V Serga
- The European Drosophila Population Genomics Consortium (DrosEU)
- National Antarctic Scientific Center of Ukraine, 16 Shevchenko Avenue, Kyiv, 01601, Ukraine
- Taras Shevchenko National University of Kyiv, 64 Volodymyrska str, Kyiv 01601, Ukraine
| | - Marina Stamenkovic-Radak
- The European Drosophila Population Genomics Consortium (DrosEU)
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, Serbia
| | - Marija Tanaskovic
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute for Biological Research “Sinisa Stankovic”, National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia
| | - Marija Savic Veselinovic
- The European Drosophila Population Genomics Consortium (DrosEU)
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, Serbia
| | - Jorge Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, i3S, Porto, Portugal
| | - Cristina P Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, i3S, Porto, Portugal
| | - Martin Kapun
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Division of Cell & Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Thomas Flatt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Fribourg, Fribourg CH-1700, Switzerland
| | - Josefa González
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Fabian Staubach
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolution and Ecology, University of Freiburg, Freiburg 79104, Germany
| | - Darren J Obbard
- The European Drosophila Population Genomics Consortium (DrosEU)
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
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4
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Loiseau V, Herniou EA, Moreau Y, Lévêque N, Meignin C, Daeffler L, Federici B, Cordaux R, Gilbert C. Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses. Virus Evol 2020; 6:vez060. [PMID: 32002191 PMCID: PMC6983493 DOI: 10.1093/ve/vez060] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Our knowledge of the diversity and frequency of genomic structural variation segregating in populations of large double-stranded (ds) DNA viruses is limited. Here, we sequenced the genome of a baculovirus (Autographa californica multiple nucleopolyhedrovirus [AcMNPV]) purified from beet armyworm (Spodoptera exigua) larvae at depths >195,000× using both short- (Illumina) and long-read (PacBio) technologies. Using a pipeline relying on hierarchical clustering of structural variants (SVs) detected in individual short- and long-reads by six variant callers, we identified a total of 1,141 SVs in AcMNPV, including 464 deletions, 443 inversions, 160 duplications, and 74 insertions. These variants are considered robust and unlikely to result from technical artifacts because they were independently detected in at least three long reads as well as at least three short reads. SVs are distributed along the entire AcMNPV genome and may involve large genomic regions (30,496 bp on average). We show that no less than 39.9 per cent of genomes carry at least one SV in AcMNPV populations, that the vast majority of SVs (75%) segregate at very low frequency (<0.01%) and that very few SVs persist after ten replication cycles, consistent with a negative impact of most SVs on AcMNPV fitness. Using short-read sequencing datasets, we then show that populations of two iridoviruses and one herpesvirus are also full of SVs, as they contain between 426 and 1,102 SVs carried by 52.4–80.1 per cent of genomes. Finally, AcMNPV long reads allowed us to identify 1,757 transposable elements (TEs) insertions, 895 of which are truncated and occur at one extremity of the reads. This further supports the role of baculoviruses as possible vectors of horizontal transfer of TEs. Altogether, we found that SVs, which evolve mostly under rapid dynamics of gain and loss in viral populations, represent an important feature in the biology of large dsDNA viruses.
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Affiliation(s)
- Vincent Loiseau
- Laboratoire Evolution, Génomes, Comportement, Écologie, Unité Mixte de Recherche 9191 Centre National de la Recherche Scientifique et Unité Mixte de Recherche 247 Institut de Recherche pour le Développement, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS - Université de Tours, 37200 Tours, France
| | - Yannis Moreau
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS - Université de Tours, 37200 Tours, France
| | - Nicolas Lévêque
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, 86000 Poitiers, France.,Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, EA 4331, Université de Poitiers, 86000 Poitiers, France
| | - Carine Meignin
- Modèles Insectes d'Immunité Innée (M3i), Université de Strasbourg, IBMC CNRS-UPR9022, Strasbourg F-67000, France
| | - Laurent Daeffler
- Modèles Insectes d'Immunité Innée (M3i), Université de Strasbourg, IBMC CNRS-UPR9022, Strasbourg F-67000, France
| | - Brian Federici
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, 86000 Poitiers, France
| | - Clément Gilbert
- Laboratoire Evolution, Génomes, Comportement, Écologie, Unité Mixte de Recherche 9191 Centre National de la Recherche Scientifique et Unité Mixte de Recherche 247 Institut de Recherche pour le Développement, Université Paris-Saclay, Gif-sur-Yvette 91198, France
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5
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Ascovirus P64 Homologs: A Novel Family of Large Cationic Proteins That Condense Viral Genomic DNA for Encapsidation. BIOLOGY 2018; 7:biology7030044. [PMID: 30208603 PMCID: PMC6163548 DOI: 10.3390/biology7030044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/01/2018] [Accepted: 09/07/2018] [Indexed: 01/05/2023]
Abstract
Eukaryotic dsDNA viruses use small basic protamine-like proteins or histones, typically <15 kDa, to condense and encapsidate their genomic (g)DNAs during virogenesis. Ascoviruses are large dsDNA (~100⁻200 kbp) viruses that are pathogenic to lepidopteran larvae. Little is known about the molecular basis for condensation and encapsidation of their gDNAs. Previous proteomic analysis showed that Spodoptera frugiperda ascovirus (SfAV-1a) virions contain a large unique DNA-binding protein (P64; 64 kDa, pI = 12.2) with a novel architecture proposed to condense its gDNA. Here we used physical, biochemical, and transmission electron microscopy techniques to demonstrate that P64's basic C-terminal domain condenses SfAV-1a gDNA. Moreover, we demonstrate that only P64 homologs in other ascovirus virions are unique in stably binding DNA. As similar protein families or subfamilies were not identified in extensive database searches, our collective data suggest that ascovirus P64 homologs comprise a novel family of atypical large viral gDNA condensing proteins.
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6
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Qiu L, Chen MM, Wan XY, Zhang QL, Li C, Dong X, Yang B, Huang J. Detection and quantification of shrimp hemocyte iridescent virus by TaqMan probe based real-time PCR. J Invertebr Pathol 2018; 154:95-101. [DOI: 10.1016/j.jip.2018.04.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 04/10/2018] [Accepted: 04/12/2018] [Indexed: 12/26/2022]
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7
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Invertebrate Iridoviruses: A Glance over the Last Decade. Viruses 2018; 10:v10040161. [PMID: 29601483 PMCID: PMC5923455 DOI: 10.3390/v10040161] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 02/06/2023] Open
Abstract
Members of the family Iridoviridae (iridovirids) are large dsDNA viruses that infect both invertebrate and vertebrate ectotherms and whose symptoms range in severity from minor reductions in host fitness to systemic disease and large-scale mortality. Several characteristics have been useful for classifying iridoviruses; however, novel strains are continuously being discovered and, in many cases, reliable classification has been challenging. Further impeding classification, invertebrate iridoviruses (IIVs) can occasionally infect vertebrates; thus, host range is often not a useful criterion for classification. In this review, we discuss the current classification of iridovirids, focusing on genomic and structural features that distinguish vertebrate and invertebrate iridovirids and viral factors linked to host interactions in IIV6 (Invertebrate iridescent virus 6). In addition, we show for the first time how complete genome sequences of viral isolates can be leveraged to improve classification of new iridovirid isolates and resolve ambiguous relations. Improved classification of the iridoviruses may facilitate the identification of genus-specific virulence factors linked with diverse host phenotypes and host interactions.
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Toenshoff ER, Fields PD, Bourgeois YX, Ebert D. The End of a 60-year Riddle: Identification and Genomic Characterization of an Iridovirus, the Causative Agent of White Fat Cell Disease in Zooplankton. G3 (BETHESDA, MD.) 2018; 8:1259-1272. [PMID: 29487186 PMCID: PMC5873915 DOI: 10.1534/g3.117.300429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/08/2018] [Indexed: 12/11/2022]
Abstract
The planktonic freshwater crustacean of the genus Daphnia are a model system for biomedical research and, in particular, invertebrate-parasite interactions. Up until now, no virus has been characterized for this system. Here we report the discovery of an iridovirus as the causative agent of White Fat Cell Disease (WFCD) in Daphnia WFCD is a highly virulent disease of Daphnia that can easily be cultured under laboratory conditions. Although it has been studied from sites across Eurasia for more than 60 years, its causative agent had not been described, nor had an iridovirus been connected to WFCD before now. Here we find that an iridovirus-the Daphnia iridescent virus 1 (DIV-1)-is the causative agent of WFCD. DIV-1 has a genome sequence of about 288 kbp, with 39% G+C content and encodes 367 predicted open reading frames. DIV-1 clusters together with other invertebrate iridoviruses but has by far the largest genome among all sequenced iridoviruses. Comparative genomics reveal that DIV-1 has apparently recently lost a substantial number of unique genes but has also gained genes by horizontal gene transfer from its crustacean host. DIV-1 represents the first invertebrate iridovirus that encodes proteins to purportedly cap RNA, and it contains unique genes for a DnaJ-like protein, a membrane glycoprotein and protein of the immunoglobulin superfamily, which may mediate host-pathogen interactions and pathogenicity. Our findings end a 60-year search for the causative agent of WFCD and add to our knowledge of iridovirus genomics and invertebrate-virus interactions.
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Affiliation(s)
- Elena R Toenshoff
- Basel University, Department of Environmental Sciences, Zoology, Vesalgasse 1, CH-4051 Basel, Switzerland
| | - Peter D Fields
- Basel University, Department of Environmental Sciences, Zoology, Vesalgasse 1, CH-4051 Basel, Switzerland
| | - Yann X Bourgeois
- Basel University, Department of Environmental Sciences, Zoology, Vesalgasse 1, CH-4051 Basel, Switzerland
| | - Dieter Ebert
- Basel University, Department of Environmental Sciences, Zoology, Vesalgasse 1, CH-4051 Basel, Switzerland
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9
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Qiu L, Chen MM, Wang RY, Wan XY, Li C, Zhang QL, Dong X, Yang B, Xiang JH, Huang J. Complete genome sequence of shrimp hemocyte iridescent virus (SHIV) isolated from white leg shrimp, Litopenaeus vannamei. Arch Virol 2018; 163:781-785. [PMID: 29181623 PMCID: PMC5814465 DOI: 10.1007/s00705-017-3642-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/02/2017] [Indexed: 12/13/2022]
Abstract
Infection with shrimp hemocyte iridescent virus (SHIV), a new virus of the family Iridoviridae isolated in China, results in a high mortality rate in white leg shrimp (Litopenaeus vannamei). The complete genome sequence of SHIV was determined and analyzed in this study. The genomic DNA was 165,809 bp long with 34.6% G+C content and 170 open reading frames (ORFs). Dotplot analysis showed that the longest repetitive region was 320 bp in length, including 11 repetitions of an 18-bp sequence and 3.1 repetitions of a 39-bp sequence. Two phylogenetic trees were constructed based on 27 or 16 concatenated sequences of proteins encoded by genes that are conserved between SHIV homologous and other iridescent viruses. The results of this study, suggest that SHIV should be considered a member of the proposed new genus "Xiairidovirus".
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Affiliation(s)
- Liang Qiu
- Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Shanghai Ocean University, Shanghai, 201306, China
| | - Meng-Meng Chen
- Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Shanghai Ocean University, Shanghai, 201306, China
| | - Ruo-Yu Wang
- Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Dalian Ocean University, Dalian, 116023, China
| | - Xiao-Yuan Wan
- Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Chen Li
- Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Qing-Li Zhang
- Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Shanghai Ocean University, Shanghai, 201306, China
| | - Xuan Dong
- Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Bing Yang
- Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Jian-Hai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jie Huang
- Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
- Shanghai Ocean University, Shanghai, 201306, China.
- Dalian Ocean University, Dalian, 116023, China.
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10
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Chen H, Zhang W, Li X, Pan Y, Yan S, Wang Y. The genome of a prasinoviruses-related freshwater virus reveals unusual diversity of phycodnaviruses. BMC Genomics 2018; 19:49. [PMID: 29334892 PMCID: PMC5769502 DOI: 10.1186/s12864-018-4432-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/03/2018] [Indexed: 11/10/2022] Open
Abstract
Background Phycodnaviruses are widespread algae-infecting large dsDNA viruses and presently contain six genera: Chlorovirus, Prasinovirus, Prymnesiovirus, Phaeovirus, Coccolithovirus and Raphidovirus. The members in Prasinovirus are identified as marine viruses due to their marine algal hosts, while prasinovirus freshwater relatives remain rarely reported. Results Here we present the complete genomic sequence of a novel phycodnavirus, Dishui Lake Phycodnavirus 1 (DSLPV1), which was assembled from Dishui Lake metagenomic datasets. DSLPV1 harbors a linear genome of 181,035 bp in length (G + C content: 52.7%), with 227 predicted genes and 2 tRNA encoding regions. Both comparative genomic and phylogenetic analyses indicate that the freshwater algal virus DSLPV1 is closely related to the members in Prasinovirus, a group of marine algae infecting viruses. In addition, a complete eukaryotic histone H3 variant was identified in the genome of DSLPV1, which is firstly detected in phycodnaviruses and contributes to understand the interaction between algal virus and its eukaryotic hosts. Conclusion It is in a freshwater ecosystem that a novel Prasinovirus-related viral complete genomic sequence is discovered, which sheds new light on the evolution and diversity of the algae infecting Phycodnaviridae. Electronic supplementary material The online version of this article (10.1186/s12864-018-4432-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Chen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Weijia Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Present address: Archaea Center, Department of Biology, Copenhagen University, DK2000, Copenhagen, Denmark
| | - Xiefei Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China
| | - Shuling Yan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Institute of Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. .,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China.
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11
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Li F, Xu L, Yang F. Genomic characterization of a novel iridovirus from redclaw crayfish Cherax quadricarinatus: evidence for a new genus within the family Iridoviridae. J Gen Virol 2017; 98:2589-2595. [DOI: 10.1099/jgv.0.000904] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Fang Li
- State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of State Oceanic Administration, Third Institute of Oceanography, SOA, Xiamen 361005, PR China
| | - Limei Xu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of State Oceanic Administration, Third Institute of Oceanography, SOA, Xiamen 361005, PR China
| | - Feng Yang
- State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of State Oceanic Administration, Third Institute of Oceanography, SOA, Xiamen 361005, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
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12
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Characterization of a new member of Iridoviridae, Shrimp hemocyte iridescent virus (SHIV), found in white leg shrimp (Litopenaeus vannamei). Sci Rep 2017; 7:11834. [PMID: 28928367 PMCID: PMC5605518 DOI: 10.1038/s41598-017-10738-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/14/2017] [Indexed: 11/08/2022] Open
Abstract
A newly discovered iridescent virus that causes severe disease and high mortality in farmed Litopenaeus vannamei in Zhejiang, China, has been verified and temporarily specified as shrimp hemocyte iridescent virus (SHIV). Histopathological examination revealed basophilic inclusions and pyknosis in hematopoietic tissue and hemocytes in gills, hepatopancreas, periopods and muscle. Using viral metagenomics sequencing, we obtained partial sequences annotated as potential iridoviridae. Phylogenetic analyses using amino acid sequences of major capsid protein (MCP) and ATPase revealed that it is a new iridescent virus but does not belong to the five known genera of Iridoviridae. Transmission electron microscopy showed that the virus exhibited a typical icosahedral structure with a mean diameter of 158.6 ± 12.5 nm (n = 30)(v-v) and 143.6 ± 10.8 nm (n = 30)(f-f), and an 85.8 ± 6.0 nm (n = 30) nucleoid. Challenge tests of L. vannamei via intermuscular injection, per os and reverse gavage all exhibited 100% cumulative mortality rates. The in situ hybridization showed that hemopoietic tissue, gills, and hepatopancreatic sinus were the positively reacting tissues. Additionally, a specific nested PCR assay was developed. PCR results revealed that L. vannamei, Fenneropenaeus chinensis, and Macrobrachium rosenbergii were SHIV-positive, indicating a new threat existing in the shrimp farming industry in China.
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13
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İnce İA, Pijlman GP, Vlak JM, van Oers MM. Hairpin structures with conserved sequence motifs determine the 3' ends of non-polyadenylated invertebrate iridovirus transcripts. Virology 2017; 511:344-353. [PMID: 28709684 DOI: 10.1016/j.virol.2017.06.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
Previously, we observed that the transcripts of Invertebrate iridescent virus 6 (IIV6) are not polyadenylated, in line with the absence of canonical poly(A) motifs (AATAAA) downstream of the open reading frames (ORFs) in the genome. Here, we determined the 3' ends of the transcripts of fifty-four IIV6 virion protein genes in infected Drosophila Schneider 2 (S2) cells. By using ligation-based amplification of cDNA ends (LACE) it was shown that the IIV6 mRNAs often ended with a CAUUA motif. In silico analysis showed that the 3'-untranslated regions of IIV6 genes have the ability to form hairpin structures (22-56 nt in length) and that for about half of all IIV6 genes these 3' sequences contained complementary TAATG and CATTA motifs. We also show that a hairpin in the 3' flanking region with conserved sequence motifs is a conserved feature in invertebrate-infecting iridoviruses (genus Iridovirus and Chloriridovirus).
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Affiliation(s)
- İkbal Agah İnce
- Department of Medical Microbiology, Acıbadem University Medical School, Atasehir, 34752 Istanbul, Turkey.
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Just M Vlak
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Monique M van Oers
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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14
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Diversity of large DNA viruses of invertebrates. J Invertebr Pathol 2017; 147:4-22. [DOI: 10.1016/j.jip.2016.08.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 11/17/2022]
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15
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Dizman YA, Muratoglu H, Sandalli C, Nalcacioglu R, Demirbag Z. Chilo iridescent virus (CIV) ORF 012L encodes a protein with both exonuclease and endonuclease functions. Arch Virol 2016; 161:3029-37. [PMID: 27496102 DOI: 10.1007/s00705-016-3007-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/01/2016] [Indexed: 10/21/2022]
Abstract
Chilo iridescent virus (CIV) is the type member of the genus Iridovirus within the family Iridoviridae. The virions of CIV contain a single linear dsDNA molecule that is circularly permuted and terminally redundant. The genome of CIV contains an open reading frame (ORF 012L) encoding a protein homologous to exonuclease II of Schizosaccharomyces pombe. In this study, we focused on the characterization of CIV ORF 012L. The target ORF was cloned into the pET28a vector, expressed in E. coli strain BL21 (DE3) pLysS with an N-terminal His tag and purified to homogeneity by using Ni-NTA affinity chromatography. Biochemical characterization of the purified CIV 012L confirmed that this viral protein is a functional 5'-3' exonuclease that digests 3'-biotin-labelled oligonucleotides and linear double-stranded DNA (dsDNA) molecules from their 5' termini in a highly processive manner. CIV 012L also has a potent endonuclease activity on dsDNA in vitro. In addition, CIV 012L converted supercoiled plasmid DNA (replicative form I, RFI) into the open circular form (RFII) and then open circular form into linear form (RFIII). Endonuclease activity of CIV 012L was optimal in the presence of 10 mM Mg(2+) or 30 mM Mn(2+) ions and at 150 mM NaCl or KCl salt concentrations. The highest endonuclease activity was obtained at pH 8, and it reached a maximum at 55 °C. The CIV 012L protein showed deficiencies for both double- and single-stranded RNAs.
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Affiliation(s)
- Yesim Akturk Dizman
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey.,Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, 53100, Rize, Turkey
| | - Hacer Muratoglu
- Department of Molecular Biology and Genetic, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Cemal Sandalli
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, 53100, Rize, Turkey
| | - Remziye Nalcacioglu
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey.
| | - Zihni Demirbag
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
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16
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Webster CL, Longdon B, Lewis SH, Obbard DJ. Twenty-Five New Viruses Associated with the Drosophilidae (Diptera). Evol Bioinform Online 2016; 12:13-25. [PMID: 27375356 PMCID: PMC4915790 DOI: 10.4137/ebo.s39454] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/21/2016] [Accepted: 04/23/2016] [Indexed: 01/19/2023] Open
Abstract
Drosophila melanogaster is an important laboratory model for studies of antiviral immunity in invertebrates, and Drosophila species provide a valuable system to study virus host range and host switching. Here, we use metagenomic RNA sequencing of about 1600 adult flies to discover 25 new RNA viruses associated with six different drosophilid hosts in the wild. We also provide a comprehensive listing of viruses previously reported from the Drosophilidae. The new viruses include Iflaviruses, Rhabdoviruses, Nodaviruses, and Reoviruses, and members of unclassified lineages distantly related to Negeviruses, Sobemoviruses, Poleroviruses, Flaviviridae, and Tombusviridae. Among these are close relatives of Drosophila X virus and Flock House virus, which we find in association with wild Drosophila immigrans. These two viruses are widely used in experimental studies but have not been previously reported to naturally infect Drosophila. Although we detect no new DNA viruses, in D. immigrans and Drosophila obscura, we identify sequences very closely related to Armadillidium vulgare iridescent virus (Invertebrate iridescent virus 31), bringing the total number of DNA viruses found in the Drosophilidae to three.
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Affiliation(s)
- Claire L. Webster
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
- Evolution, behaviour and environment, School of Life Sciences, University of Sussex, Brighton, UK
| | - Ben Longdon
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Samuel H. Lewis
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Darren J. Obbard
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
- Centre for Immunity, Infection and Evolution, The University of Edinburgh, Edinburgh, UK
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17
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Xu L, Wang T, Li F, Yang F. Isolation and preliminary characterization of a new pathogenic iridovirus from redclaw crayfish Cherax quadricarinatus. DISEASES OF AQUATIC ORGANISMS 2016; 120:17-26. [PMID: 27304867 DOI: 10.3354/dao03007] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report the preliminary characterization of a new iridovirus detected in diseased Cherax quadricarinatus collected from a farm in Fujian, China. Transmission electron microscopy identified numerous icosahedral particles (~150 nm in diameter) in the cytoplasm and budding from the plasma membrane of hematopoietic tissue cells. SDS-PAGE of virions semi-purified from the hemolymph of moribund C. quadricarinatus identified 24 proteins including a 50 kDa major capsid protein (MCP). By summing the sizes of DNA restriction endonuclease fragments, the viral genome was estimated to be ~150 kb in length. A 34 amino acid sequence deduced from a 103 bp MCP gene region amplified by PCR using degenerate primers targeted to MCP gene regions conserved among iridoviruses and chloriridoviruses was most similar (55% identity) to Sergestid iridovirus. Based on virion morphology, protein composition, DNA genome length, and MCP sequence relatedness, the virus identified has tentatively been named Cherax quadricarinatus iridovirus (CQIV). In addition, experimental infection of healthy C. quadricarinatus, Procambarus clarkii, and Litopenaeus vannamei with CQIV caused the same disease and high mortality, suggesting that CQIV poses a potential threat to cultured and wild crayfish and shrimp.
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Affiliation(s)
- Limei Xu
- Key Laboratory of Marine Genetic Resources, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
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18
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Huang Y, Li S, Zhao Q, Pei G, An X, Guo X, Zhou H, Zhang Z, Zhang J, Tong Y. Isolation and characterization of a novel invertebrate iridovirus from adult Anopheles minimus (AMIV) in China. J Invertebr Pathol 2015; 127:1-5. [PMID: 25637833 DOI: 10.1016/j.jip.2015.01.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 12/01/2022]
Abstract
An invertebrate iridovirus (designated AMIV) was isolated from adult wild-captured Anopheles minimus mosquitoes in China. AMIV was pathologically and morphologically characterized and sequenced using the Ion Torrent™ sequencing platform. Phylogenetic analysis based on both the major capsid protein and core genes revealed that AMIV differs from all the members of the family Iridoviridae. The AMIV negatively strained virion has a diameter of about 130nm. AMIV contains a linear DNA molecule of 163,023bp, with 39% G+C content and 148 coding sequences. The genome analysis revealed that AMIV genome encodes a high content of replication associated genes including BRO-like genes. This is the ninth complete genome of IIV reported.
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Affiliation(s)
- Yong Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing 100071, China
| | - Shasha Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing 100071, China
| | - Qiumin Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing 100071, China
| | - Guangqian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing 100071, China
| | - Xiaoping An
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing 100071, China
| | - Xiaofang Guo
- Yunnan Institute of Parasitic Diseases, Pu'er, Yunnan, China
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Pu'er, Yunnan, China
| | - Zhiyi Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing 100071, China
| | - Jiusong Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing 100071, China.
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing 100071, China.
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19
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Piégu B, Asgari S, Bideshi D, Federici BA, Bigot Y. Evolutionary relationships of iridoviruses and divergence of ascoviruses from invertebrate iridoviruses in the superfamily Megavirales. Mol Phylogenet Evol 2015; 84:44-52. [PMID: 25562178 DOI: 10.1016/j.ympev.2014.12.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 10/09/2014] [Accepted: 12/19/2014] [Indexed: 12/29/2022]
Abstract
The family Iridoviridae of the superfamily Megavirales currently consists of five genera. Three of these, Lymphocystivirus, Megalocytivirus and Ranavirus, are composed of species that infect vertebrates, and the other two, Chloriridovirus and Iridovirus, contain species that infect invertebrates. Until recently, the lack of genomic sequence data limited investigation of the evolutionary relationships between the invertebrate iridoviruses (IIVs) and vertebrate iridoviruses (VIVs), as well as the relationship of these viruses to those of the closely related family Ascoviridae, which only contains species that infect insects. To help clarify the phylogenetic relationships of these viruses, we recently published the annotated genome sequences of five additional IIV isolates. Here, using classical approaches of phylogeny via maximum likelihood, a Bayesian approach, and resolution of a core protein tree, we demonstrate that the invertebrate and vertebrate IV species constitute two lineages that diverged early during the evolution of the family Iridoviridae, before the emergence of the four IIV clades, previously referred to as Chloriridoviruses, Polyiridoviruses, Oligoiridoviruses and Crustaceoiridoviruses. In addition, we provide evidence that species of the family Ascoviridae have a more recent origin than most iridoviruses, emerging just before the differentiation between the Oligoiridoviruses and Crustaceoiridovirus clades. Our results also suggest that after emergence, based on their molecular clock, the ascoviruses evolved more quickly than their closest iridovirus relatives.
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Affiliation(s)
- Benoît Piégu
- UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, 37380 Nouzilly, France
| | - Sassan Asgari
- UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, 37380 Nouzilly, France; School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dennis Bideshi
- California Baptist University, Department of Natural and Mathematical Sciences, 8432 Magnolia Avenue, Riverside, CA 92504, USA; Department of Entomology and Developmental Biology, University of California, Riverside, CA 92521, USA
| | - Brian A Federici
- Department of Entomology and Developmental Biology, University of California, Riverside, CA 92521, USA; Interdepartmental Graduate Programs in Microbiology and Cell, Molecular and Developmental Biology, University of California, Riverside, CA 92521, USA
| | - Yves Bigot
- UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, 37380 Nouzilly, France.
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20
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Ozgen A, Muratoglu H, Demirbag Z, Vlak JM, van Oers MM, Nalcacioglu R. Construction and characterization of a recombinant invertebrate iridovirus. Virus Res 2014; 189:286-92. [PMID: 24930447 DOI: 10.1016/j.virusres.2014.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 05/09/2014] [Accepted: 05/13/2014] [Indexed: 01/04/2023]
Abstract
Chilo iridescent virus (CIV), officially named Insect iridescent virus 6 (IIV6), is the type species of the genus Iridovirus (family Iridoviridae). In this paper we constructed a recombinant CIV, encoding the green fluorescent protein (GFP). This recombinant can be used to investigate viral replication dynamics. We showed that homologous recombination is a valid method to make CIV gene knockouts and to insert foreign genes. The CIV 157L gene, putatively encoding a non-functional inhibitor of apoptosis (IAP), was chosen as target for foreign gene insertion. The gfp open reading frame preceded by the viral mcp promoter was inserted into the 157L locus by homologous recombination in Anthonomus grandis BRL-AG-3A cells. Recombinant virus (rCIV-Δ157L-gfp) was purified by successive rounds of plaque purification. All plaques produced by the purified recombinant virus emitted green fluorescence due to the presence of GFP. One-step growth curves for recombinant and wild-type CIV were similar and the recombinant was fully infectious in vivo. Hence, CIV157L can be inactivated without altering the replication kinetics of the virus. Consequently, the CIV 157L locus can be used as a site for insertion of foreign DNA, e.g. to modify viral properties for insect biocontrol.
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Affiliation(s)
- Arzu Ozgen
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey
| | - Hacer Muratoglu
- Karadeniz Technical University, Faculty of Science, Department of Molecular Biology and Genetics, 61080 Trabzon, Turkey
| | - Zihni Demirbag
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey
| | - Just M Vlak
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Monique M van Oers
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Remziye Nalcacioglu
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey.
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